Aims: To compare retinal nerve fiber layer (RNFL) thickness and choroidal thickness in patients with exfoliation syndrome (XFS) and exfoliative glaucoma (XFG) for 1–5 years or 6–10 years compared to healthy volunteers. Methods and Material: Seventy-eight eyes of 78 patients with XFG, 78 eyes of 78 patients with XFS, and 83 eyes of 83 healthy individuals were included in this prospective study. SD-OCT data for choroid thickness and RNFL were recorded. Results: RNFL thickness was statistically significantly lower in eyes with XFG and XFS than in the control group (p < 0.001). Macular choroidal thickness decreased significantly in the XFG group compared to the XFS and control groups (p < 0.001). No significant difference was observed between the XFS and control groups (p > 0.05). In terms of choroidal and RNFL thicknesses by years in XFG and XFS patients, values were lower in the patients diagnosed 6–10 years previously than in those diagnosed 1–5 years previously. However, the difference was not statistically significant (p > 0.05). Conclusions: Thinning of both choroidal and RNLF thickness in XFG and XFS patients may mean that PEX material is an important risk factor for the progression of XFS to XFG. In addition, thinner choroid and RNLF thickness in the 6–10 years groups show the effect of PEX material and the importance of time.